Have you considered a retractable wall for the main bays? It would never hurt to be able to open up the floor if you needed to. I hope you are not offended , but I re-worked your plan a little bit. The dotted line between the bays represents the retractable or partitian wall. The wall between the main bays has been moved to the west 1 bay to seperate the main floor from the other rooms. I also opened up the bay doors to about 10'wide.
I know you have your design well thought out , I was just throwin out ideers. When you have your trusses built , keep overhead storage in mind as an option.I see lots of good wasted space up there all the time.
Edit:
Just thought of this. Have you considered an in floor pit for easy oil changes , etc? It's not the solution to everything under the car , but may be an alternative to a lift in some situations. You could also use "cathedral" or vaulted trusses in the garage area to improve headroom for a lift.